Other useful paper from Chris... [
https://cdn-pubs.acs.org/doi/10.1021/ct400273t]
Best
Matias
----- Mensaje original -----
De: "Matias Machado" <mmachado.pasteur.edu.uy>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Sábado, 11 de Agosto 2018 17:06:43
Asunto: Re: [AMBER] Restraints on a system
Dear Debarati,
As far as I know AMBER can't apply positional restrains on individual coordinates (x, y or z) as GROMACS can do... (which is very useful for equilibrating membranes)
Nevertheless, I don't think that is the correct way to go on your problem... as you would be restricting the protein tumbling and translation the resulting conformation will be highly dependent on the initial system's conformation... not to mention that you would be introducing artificial forces on the system to number some issues...
If you want to accelerate the sampling on a particular reaction coordinate for study a given phenomena then you should explore other MD techniques rather than a plane simulation...
For example, take a look at this paper from Christopher Chipot's group [
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791]
Read the AMBER manual for available options... other techniques can be perform on AMBER though PLUMED [
http://www.plumed.org]
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/laboratorios-eng/lsbm]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Debarati DasGupta" <debarati_dasgupta.hotmail.com>
Para: amber.ambermd.org, "david case" <david.case.rutgers.edu>
Enviados: Martes, 7 de Agosto 2018 18:15:06
Asunto: [AMBER] Restraints on a system
How to go about putting restraints in a MD considering 2 proteins.
I have 2 proteins which want to dimerize and I am studying the mechanism of dimerization.
I want to set up a amber simulation whereby the monomers are separated by a distance of 10/12 Angstroms and during the course of simulation I want to check if they are coming closer to dimerize or not.
To do this, I want to restrict any kind of motion in the y and z directions so that the only motion the molecules denote is in the x direction.
How to implement in amber 16 input file.
Pls help.
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Received on Sat Aug 11 2018 - 13:30:04 PDT
